LBB5 may as well be a different game.
So many LBB:2 and LBB:3 paradigms are changed by it that the contradictions make for a totally different setting.
LBB1-3 may be a unit, and treatable as a standalone component, but that idempotence vanishes one the supplements are incorporated. The supplements are not orthogonal to the whole, like, say, and adventure is. Rather they're an evolution of it. This is clear both in the industry, as well as later demonstrated when the games were consolidated.
Consider: Squad Leader is a different game when Cross of Iron is added to it. SFB morphed dramatically as the supplements were released. Both of them went through a serious consolidation phase that incorporated all of the supplements in to a more integrated whole.
Arguably, MT was that for CT. Not so much a rewrite, as an integration of the published works. All of the learning that happened through the development of the CT game system, along with the Imperium, combined in to a single, reorganized kit.
So, it's fair to consider LBB1-3 as a singular entity, but the Supplement reach their tendrils back, and affect that unit.
My first point is that the Imperium and the attendant Books and Supplements had not been created along with Books 1-3 in some sort of grand plan.
No, but it's clear that they weren't developing new products from a clean slate, and in isolation. Rather they were developing the whole, with the publications of the rules, boardgames, and JTAS articles being essentially snapshots of their train of thought at the time of publishing.
They may not have had envisioned such a whole at the very start, but that shifted, and reasonably quickly, for both commercial and, I assume, personal interest of the developers. That is, an 11,000 system spanning Imperium didn't just happen, They(tm) wanted it that way. When that concept became a gleam in their eye, anyone can guess.
So it's fair to consider the texts as simply manifestations of their evolving continuum, rather than isolated constructs.
It's also clear that this is the "galaxy they wanted", as they simply double downed on it when they created MT.